2-74428935-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001015055.2(RTKN):c.763C>T(p.Arg255Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,613,638 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R255H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001015055.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTKN | NM_001015055.2 | c.763C>T | p.Arg255Cys | missense_variant | 7/12 | ENST00000272430.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTKN | ENST00000272430.10 | c.763C>T | p.Arg255Cys | missense_variant | 7/12 | 1 | NM_001015055.2 | P4 | |
RTKN | ENST00000233330.6 | c.613C>T | p.Arg205Cys | missense_variant | 7/12 | 1 | |||
RTKN | ENST00000305557.9 | c.724C>T | p.Arg242Cys | missense_variant | 8/13 | 5 | A1 | ||
RTKN | ENST00000640304.2 | c.763C>T | p.Arg255Cys | missense_variant | 7/12 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251128Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135746
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461336Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727002
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 22, 2023 | The c.763C>T (p.R255C) alteration is located in exon 7 (coding exon 7) of the RTKN gene. This alteration results from a C to T substitution at nucleotide position 763, causing the arginine (R) at amino acid position 255 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at